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International Journal of Systematic and... Oct 2021A novel species of the genus , designated SYSU M41301, was isolated from water sample of the Pearl River estuary in Guangdong, China. Polyphasic, taxonomic and...
A novel species of the genus , designated SYSU M41301, was isolated from water sample of the Pearl River estuary in Guangdong, China. Polyphasic, taxonomic and phylogenomic analyses were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU M41301 showed the highest sequence similarity to KCTC 22213 (97.9 %) and KCTC 23339 (96.4 %). The novel species could be differentiated from other species of the genus by its distinct phenotypic and genotypic characteristics. The isolate was Gram-staining-negative, aerobic, short rod-shape, oxidase-positive and non-motile. The predominant respiratory quinone was ubiquinone 8 (Q-8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and one unidentified polar lipid. The major fatty acids (>10 % of total) were 11-methyl C 7, summed feature 3 (C c / or C c) and summed feature 8 (C 7 and/or C 6). The G+C content of the novel isolate based on genomic DNA was 72.0 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU M41301 should be considered to represent a novel species in the genus for which the name sp. nov. is proposed with the type strain SYSU M41301 (=KCTC 72726=CGMCC 1.18613).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Estuaries; Fatty Acids; Methylobacteriaceae; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Rivers; Sequence Analysis, DNA; Ubiquinone
PubMed: 34623235
DOI: 10.1099/ijsem.0.004994 -
Heliyon Aug 2021f.sp. (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or...
f.sp. (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or fungicides strongly affect the soil microbiomes ecosystem. Suppressive soil is a promising method for controlling soil-borne pathogens in which soil microbiomes may affect the suppressiveness. The comparative analysis of microbial diversity was conducted from suppressive and conducive soils by analyzing whole shotgun metagenomic DNA data. Two suppressive soil samples and two conducive soil samples were collected from a banana plantation in Sukabumi, West Java, Indonesia. Each soil sample was prepared by mixing the soil samples collected from three points sampling sites with 20 cm depth. Analysis of microbial abundance, diversity, co-occurrence network using Metagenome Analyzer 6 (MEGAN6) and functional analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed. Data showed the abundance of s, and were higher in the suppressive than conducive soils. Interestingly, those bacteria groups are known functionally as members of Plant Growth Promoting Rhizobacteria (PGPR). The co-occurrence analysis showed , and were present in the suppressive soils, while and more were found in the conducive soils. Furthermore, the relative abundance of , , , and was performed. The analysis showed that the relative abundance of and was higher in the suppressive than conducive soils. Therefore, it assumed and play a role in suppressing Foc based on co-occurrence and abundance analysis. Functional analysis of and showed that the zinc/manganese transport system was higher in the suppressive than conducive soils. In contrast, the phosphate transport system was not found in conducive soils. Both functions are may be responsible for the synthesis of a siderophore and phosphate solubilization. In conclusion, this study provides information that PGPR may be contributing to Foc growth suppressing by releasing secondary metabolites.
PubMed: 34401567
DOI: 10.1016/j.heliyon.2021.e07636 -
Molecular Microbiology Oct 2021Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as...
Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE and crtB we disrupted the production of squalene and phytoene in M. extorquens PA1, which are the presumed precursors for hopanoids and carotenoids respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C backbone, rather than the previously predicted canonical C phytoene-derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1.
Topics: Bacterial Outer Membrane; Biosynthetic Pathways; Carotenoids; Gene Knockdown Techniques; Geranylgeranyl-Diphosphate Geranylgeranyltransferase; Methylobacterium extorquens; Oxidative Stress; Oxidoreductases; Phylogeny; Planctomycetes; Sequence Deletion; Squalene
PubMed: 34387371
DOI: 10.1111/mmi.14794 -
ACS Chemical Biology Aug 2021Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific...
Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific precursor; however, this approach is limited by the availability of isotopically enriched precursors. We used an inverse stable isotopic labeling approach to identify natural products by growing bacteria on a C-carbon source and then identifying C-precursor incorporation by mass spectrometry. We applied this approach to methylotrophs, ecologically important bacteria predicted to have significant yet underexplored biosynthetic potential. We demonstrate that this method identifies acyl homoserine lactone quorum sensing signals produced by diverse methylotrophs grown on three different one-carbon compounds. We then apply this approach to simultaneously detect five previously unidentified signals produced by a methylotroph and link these compounds to their synthases. We envision that this method can be used to identify other natural product classes synthesized by methylotrophs and other organisms that grow on relatively inexpensive C-carbon sources.
Topics: Acyl-Butyrolactones; Carbon; Carbon Isotopes; Isotope Labeling; Methylobacteriaceae; Methylococcaceae; Proof of Concept Study; Quorum Sensing
PubMed: 34328722
DOI: 10.1021/acschembio.1c00329 -
Microbes and Environments 2021Nitrogen deficiency affects soybean growth and physiology, such as symbiosis with rhizobia; however, its effects on the bacterial composition of the soybean root...
Nitrogen deficiency affects soybean growth and physiology, such as symbiosis with rhizobia; however, its effects on the bacterial composition of the soybean root microbiota remain unclear. A bacterial community analysis by 16S rRNA gene amplicon sequencing showed nitrogen deficiency-induced bacterial community shifts in soybean roots with the marked enrichment of Methylobacteriaceae. The abundance of Methylobacteriaceae was low in the roots of field-grown soybean without symptoms of nitrogen deficiency. Although Methylobacteriaceae isolated from soybean roots under nitrogen deficiency did not promote growth or nodulation when inoculated into soybean roots, these results indicate that the enrichment of Methylobacteriaceae in soybean roots is triggered by nitrogen-deficiency stress.
Topics: Bacteria; DNA, Bacterial; Microbiota; Nitrogen; Plant Roots; RNA, Ribosomal, 16S; Soil; Soil Microbiology; Glycine max
PubMed: 34234044
DOI: 10.1264/jsme2.ME21004 -
Ecotoxicology and Environmental Safety Sep 2021Flonicamid (N-cyanomethyl-4-trifluoromethylnicotinamide, FLO) is a new type of pyridinecarboxamide insecticide that exhibits particularly good efficacy in pest control....
Flonicamid (N-cyanomethyl-4-trifluoromethylnicotinamide, FLO) is a new type of pyridinecarboxamide insecticide that exhibits particularly good efficacy in pest control. However, the extensive use of FLO in agricultural production poses environmental risks. Hence, its environmental behavior and degradation mechanism have received increasing attention. Microvirga flocculans CGMCC 1.16731 rapidly degrades FLO to produce the intermediate N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM) and the end acid metabolite 4-(trifluoromethyl) nicotinol glycine (TFNG). This bioconversion is mediated by the nitrile hydratase/amidase system; however, the amidase that is responsible for the conversion of TFNG-AM to TFNG has not yet been reported. Here, gene cloning, overexpression in Escherichia coli and characterization of pure enzymes showed that two amidases-AmiA and AmiB-hydrolyzed TFNG-AM to TFNG. AmiA and AmiB showed only 20-30% identity to experimentally characterized amidase signature family members, and represent novel amidases. Compared with AmiA, AmiB was more sensitive to silver and copper ions but more resistant to organic solvents. Both enzymes demonstrated good pH tolerance and exhibited broad amide substrate specificity. Homology modeling suggested that residues Asp191 and Ser195 may strongly affect the catalytic activity of AmiA and AmiB, respectively. The present study furthers our understanding of the enzymatic mechanisms of biodegradation of nitrile-containing insecticides and may aid in the development of a bioremediation agent for FLO.
Topics: Amidohydrolases; Bacterial Proteins; Biodegradation, Environmental; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Insecticides; Methylobacteriaceae; Niacinamide
PubMed: 34091185
DOI: 10.1016/j.ecoenv.2021.112384 -
PLoS Biology May 2021Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in...
Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M. extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.
Topics: Bacteria; Formaldehyde; Methylobacterium; Methylobacterium extorquens; Stress, Physiological
PubMed: 34038406
DOI: 10.1371/journal.pbio.3001208 -
Systematic and Applied Microbiology May 2021Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523 and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria...
Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523 and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria plants collected near Thessaloniki, Greece. Analysis of their 16S rRNA gene sequences revealed that they form a separate cluster related to the genus Roseomonas. A comparative whole genome analysis of the two strains and the type strains of related Roseomonas species revealed average nucleotide identity values from 78.84 and 80.32%. The G + C contents of the genomic DNA of strains LMG 31523 and LMG 31524 were 69.69% and 69.74%, respectively. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that the strains LMG 31523 and LMG 31524 represent a novel species of the genus Roseomonas. Genome analysis of the new strains showed a number of genes involved in survival in the rhizosphere environment and in plant colonization and confirmed the endophytic characteristics of LMG 31523 and LMG 31524. Since the strains LMG 31523 and LMG 31524 were isolated from a plant collected in Greece the name Roseomonas hellenica sp. nov. is proposed. The type strain is LMG 31523 (=CECT 30032).
Topics: Bacterial Typing Techniques; Base Composition; Boraginaceae; DNA, Bacterial; Endophytes; Greece; Methylobacteriaceae; Phylogeny; Pigmentation; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33945925
DOI: 10.1016/j.syapm.2021.126206 -
The Journal of Biological Chemistry 2021Methylofuran (MYFR) is a formyl-carrying coenzyme essential for the oxidation of formaldehyde in most methylotrophic bacteria. In Methylorubrum extorquens, MYFR contains...
Methylofuran (MYFR) is a formyl-carrying coenzyme essential for the oxidation of formaldehyde in most methylotrophic bacteria. In Methylorubrum extorquens, MYFR contains a large and branched polyglutamate side chain of up to 24 glutamates. These glutamates play an essential role in interfacing the coenzyme with the formyltransferase/hydrolase complex, an enzyme that generates formate. To date, MYFR has not been identified in other methylotrophs, and it is unknown whether its structural features are conserved. Here, we examined nine bacterial strains for the presence and structure of MYFR using high-resolution liquid chromatography-mass spectrometry (LC-MS). Two of the strains produced MYFR as present in M. extorquens, while a modified MYFR containing tyramine instead of tyrosine in its core structure was detected in six strains. When M. extorquens was grown in the presence of tyramine, the compound was readily incorporated into MYFR, indicating that the biosynthetic enzymes are unable to discriminate tyrosine from tyramine. Using gene deletions in combination with LC-MS analyses, we identified three genes, orf5, orfY, and orf17 that are essential for MYFR biosynthesis. Notably, the orfY and orf5 mutants accumulated short MYFR intermediates with only one and two glutamates, respectively, suggesting that these enzymes catalyze glutamate addition. Upon homologous overexpression of orf5, a drastic increase in the number of glutamates in MYFR was observed (up to 40 glutamates), further corroborating the function of Orf5 as a glutamate ligase. We thus renamed OrfY and Orf5 to MyfA and MyfB to highlight that these enzymes are specifically involved in MYFR biosynthesis.
Topics: Coenzymes; Formaldehyde; Furans; Glutamic Acid; Hydrolases; Hydroxymethyl and Formyl Transferases; Methylobacterium extorquens; Polyglutamic Acid
PubMed: 33894199
DOI: 10.1016/j.jbc.2021.100682 -
Genome Biology and Evolution Jun 2021Understanding the evolution of novel physiological traits is highly relevant for expanding the characterization and manipulation of biological systems. Acquisition of...
Understanding the evolution of novel physiological traits is highly relevant for expanding the characterization and manipulation of biological systems. Acquisition of new traits can be achieved through horizontal gene transfer (HGT). Here, we investigate drivers that promote or deter the maintenance of HGT-driven degeneracy, occurring when processes accomplish identical functions through nonidentical components. Subsequent evolution can optimize newly acquired functions; for example, beneficial alleles identified in an engineered Methylorubrum extorquens strain allowed it to utilize a "Foreign" formaldehyde oxidation pathway substituted for its Native pathway for methylotrophic growth. We examined the fitness consequences of interactions between these alleles when they were combined with the Native pathway or both (Dual) pathways. Unlike the Foreign pathway context where they evolved, these alleles were often neutral or deleterious when moved into these alternative genetic backgrounds. However, there were instances where combinations of multiple alleles resulted in higher fitness outcomes than individual allelic substitutions could provide. Importantly, the genetic context accompanying these allelic substitutions significantly altered the fitness landscape, shifting local fitness peaks and restricting the set of accessible evolutionary trajectories. These findings highlight how genetic context can negatively impact the probability of maintaining native and HGT-introduced functions together, making it difficult for degeneracy to evolve. However, in cases where the cost of maintaining degeneracy was mitigated by adding evolved alleles impacting the function of these pathways, we observed rare opportunities for pathway coevolution to occur. Together, our results highlight the importance of genetic context and resulting epistasis in retaining or losing HGT-acquired degenerate functions.
Topics: Epistasis, Genetic; Evolution, Molecular; Gene Transfer, Horizontal; Glutathione; Metabolic Networks and Pathways; Methylobacteriaceae; Plasmids
PubMed: 33885815
DOI: 10.1093/gbe/evab082